2012 Speakers

Dr. Allen’s research interests include the analysis of metabolic networks in plants by combined experimental and computational methods. These investigations give insight to plant metabolism, important for designing crops to meet future nutritional and chemical feedstock needs. Dr. Allen received his Ph.D. in engineering from Purdue University, has previously worked for the Archer Daniels Midland Company and the Great Lakes Bioenergy Research Center at Michigan State University. He joined the Danforth Center in the capacity of Research Computational Biologist with the USDA in 2010.

Dr. Antoniewicz earned his B.S. and M.S. degrees from Delft University of Technology, and his Ph.D. from Massachusetts Institute of Technology. Dr. Antoniewicz is an expert and a pioneer in the field of 13C-metabolic flux analysis (MFA). He has received several international awards for his research, including the DuPont Young Professor Award (2008) and the James E. Bailey Young Investigator Award in Metabolic Engineering (2008). His current interests are in dynamic metabolic flux analysis at metabolic non-steady state and the use of tandem mass spectrometry for flux analysis studies.

Dr. Benfey’s research focuses on plant developmental genetics and genomics. He is a fellow of the American Association for the Advancement of Science and a member of the National Academy of Sciences. Dr. Benfey received his Ph.D. from Harvard University and a DEUG (Diplome d'Etudes Universitaire Generale) from the University of Paris. He is the co-founder and CEO of GrassRoots Biotechnology, which employs a systems biology approach to discover expression elements and traits to improve agricultural and biofuel crops.

Dr. Bennetzen received his PH.D. in 1980 from the University of Washington, working in yeast molecular genetics, and began his postdoctoral research with Freeling and Walbot to study maize transposable elements (TEs). After moving to the International Plant Research Institute in 1981, he cloned the TE Mu1, and went on to show its regulation associated with DNA methylation. In 1983, he moved to Purdue University where his group identified LTR retrotransposons as the most abundant DNA in angiosperms. Since moving to the University of Georgia in 2003, his group has continued studying the mechanisms and patterns of DNA hyper-plasticity in plants.

Dr. Kenneth Birnbaum, Associate Professor of Biology, Department of Biology, Center for Genomics and Systems Biology, New York University

Dr. Birnbaum is an associate professor and a member of the Center for Genomics and Systems Biology at New York University. His work focuses on using systems biology approaches at the cell level. He has developed techniques to profile the transcriptome of single cell types and he has used these data to develop quantitative measurements of cell identity. Dr. Birnbaum applies all these techniques to studying tissue organization and cellular differentiation, using regeneration as a model. His work is funded by the NIH and NSF.

Dr. Michael Brent, Henry Edwin Sever Professor of Engineering, Department of Computer Science and Engineering, Washington University in St. Louis

Dr. Brent received a B.S. in mathematics and a Ph.D. in computer science from MIT, where his research focused on computational linguistics. He then served as Assistant and Associate Professor in the Department of Cognitive Science at Johns Hopkins, where his research focused on modeling language development in children. In 1999 he came to Washington University in St. Louis and began developing a second research program in computational biology. From 2001 to 2008 his lab focused on genome sequence analysis. Since 2008, it has focused on mapping and modeling transcriptional regulation networks and designing novel regulatory circuits.

Dr. Chang received her Ph.D. from MIT, working with JoAnne Stubbe and Daniel Nocera, and her postdoctoral training with Jay Keasling at UCB. Her research group works at the interface of enzymology and synthetic biology, with a focus on studying biological fluorine chemistry, nanoparticle synthesis by directional-sensing bacteria, and developing synthetic biofuel pathways. She has received the Dreyfus New Faculty Award, TR35 Award, Beckman Young Investigator Award, NSF CAREER Award, Agilent Early Career Award, NIH New Innovator Award, and DARPA Young Faculty Award.

Dr. Jones Prather’s research interests are centered on the design and assembly of recombinant micro-organisms for the production of small molecules, with additional efforts in novel bioprocess design approaches. Research combines the traditions of metabolic engineering with the practices of biocatalysis to expand and optimize the biosynthetic capacity of microbial systems. A particular focus is the elucidation of design principles for the production of unnatural organic compounds within the framework of the burgeoning field of synthetic biology.

Dr. Insuk Lee, Associate Professor, Yonsei University, Korea

Dr. Lee received his Ph.D. degree in Microbiology from University of Texas, Austin. During his post-doctoral research in the field of bioinformatics and systems biology, he developed a functional gene network modeling framework, which has been applied to construct genome-scale gene networks for various organisms including yeast, worm, human, Arabidopsis, rice (http://www.functionalnet.org). His current research interest focuses on network-driven biological discovery (http://www.netbiolab.org). His research is currently funded by National Research Foundation and Rural Development Administration of Korea.

Dr. Julius Lucks, Assistant Professor, School of Chemical and Biomolecular Engineering, Cornell University

Dr. Lucks received his Ph.D. in Chemical Physics from Harvard University while he was a Hertz Fellow with David Nelson. For his postdoc, he was a Miller Fellow in the laboratory of Adam Arkin at the University of California, Berkeley. The Lucks group asks fundamental questions about how RNA molecules fold and function in living organisms and how this knowledge can be used to design RNA regulators for programming biomolecular systems. To do this, they are developing SHAPE-Seq, a platform technology based on next generation sequencing that can already characterize the structures of RNA molecules in unprecedented throughput. In addition to applications in RNA synthetic biology, the Lucks group is using SHAPE-Seq to harvest RNA design principles from a variety of natural systems where RNAs play a dominant role.

Dr. June Medford, Professor, Department of Biology, Colorado State University

Dr. Medford is a leader in plant synthetic biology. She received her B.S. in Botany from the University of Maryland and Ph.D. in Biology from Yale followed by postdoctoral training with Monsanto. The Medford lab produced the first eukaryotic synthetic signal transduction pathway and has enabled a computerized detection trait in plants. Using synthetic biology, the Medford Lab has produced electronic-like control systems for plant and algal traits.

Dr. Molly Megraw, Assistant Professor, Center for Genome Research and Biocomputing, Oregon State University

Dr. Megraw received her doctoral degree in Genomics and Computational Biology from the University of Pennsylvania. During her post-doctoral work at Duke University, she developed a machine learning model which demonstrates that highly accurate gene and microRNA TSS prediction can be achieved using DNA sequence information alone. Her current work combines computational analysis of regulatory network topology with experimental methods for TSS-Seq library generation to identify over-represented regulatory circuits in the Arabidopsis thaliana root system. This September she will begin a faculty position at Oregon State University. Dr. Megraw is currently supported by an NIH K99 Pathway to Independence award.

Dr. Myers received his Ph.D. from the Department of Computer Science at Princeton University in 2007 and began his current position in 2008. Dr. Myers’s research emphasis includes computational methods for analysis and interpretation of large-scale genetic interaction networks and methods for integration of diverse genomic data to predict gene function or infer biological networks. His lab is developing approaches for analyzing and leveraging interaction networks to answer biological questions in a variety of systems including yeast, plants (Arabidopsis and maize), worm and human.

Dr. Nusinow joined the Danforth Center in March 2012. He received his B.S. in Microbiology and Molecular Genetics from University of California – Los Angeles. He obtained a Ph.D. in Biochemistry and Molecular Biology from the University of California – San Francisco.

The Nusinow laboratory is focused on understanding how the circadian clock is integrated with environmental signals to control growth, physiology and development. A combination of molecular, biochemical, genetic, genomic, and proteomic tools helps to uncover the molecular connections between signaling networks, the circadian oscillator, and specific outputs. Through combining these methods with a comparative proteomics approach, the aim is to leverage the knowledge gained from the model plant Arabidopsis to other plant species. The increased understanding of the mechanisms underlying growth and development will help improve their use as feed, food, and fuel stocks.

Dr. Sarah O’Connor, Project Leader The John Innes Centre

Dr. O’Connor received her Ph.D. from MIT in 2001 and was an Irving Sigal post-doctoral fellow at Harvard Medical School from 2001-2003. After her post-doctoral work, she became assistant and then associate professor of Chemistry at MIT. In 2011, she moved her research group to the John Innes Centre where she is a Project Leader. She is also on the faculty of the School of Chemistry at the University of East Anglia. Her research focuses on the engineering and pathway elucidation of plant-derived alkaloid natural products.

Dr. Silver received her B.S. in Chemistry and Ph.D. in Biochemistry from the University of California, was a Postdoctoral Fellow at Harvard University, and an Assistant Professor at Princeton University. Now at Harvard Medical School she is a member of the Systems Biology Department and a founding member of the Wyss Institute for Biologically Inspired Engineering. She is a Fellow of the Radcliffe Institute. Her laboratory works in Systems and Synthetic Biology on the predictable design and re-programming of biological systems and sustainability.

Dr. Smolke joined the Bioengineering Department at Stanford University as an Assistant Professor in January 2009. Professor Smolke’s research program focuses on developing modular genetic platforms for programming information processing and control functions in living systems. She has pioneered the design and application of RNA molecules that process and transmit user-specified input signals to targeted protein outputs, thereby linking molecular computation to gene expression. These technologies are leading to transformative advances in how we interact with and program biology, providing access to otherwise inaccessible information on cellular state, and allowing sophisticated control over cellular functions.

Dr. A. J. Marian Walhout, Professor, Co-Director of the Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts

Dr. Walhout is the Co-Director of the Program in Systems Biology and a Professor of Molecular Medicine at the University of Massachusetts Medical School. She has pioneered the study of the structure, function, and evolution of gene regulatory networks. Her group has developed and applied numerous experimental and computational methods, most notably high-throughput gene-centered assays for the detection of physical interactions between regulatory regions in the genome and transcription factors in different organisms, including nematodes, plants, and humans.